Hi Keith,
Adding a translator in between the 5V signals and the Cyclone III is a must, you wouldn't want a DC signal at the CIII input pins above 3.6V. For AC transitions you can go over that, but only for very brief periods of time, but still nowhere near 5.0V.
The 500 ohm series resistor sounds a bit excessive though, usually something more in the range of 25 to 50 ohms does the trick. 500 ohms would likely give more of a saw tooth waveform with slow rising and falling edges, 50 ohms will give much sharper edges and still dampen the reflections.